Matsuyama, who started the day with a four-shot lead over a quartet that included playing competitor Xander Schauffele and Masters debutant Zalatoris, carded a one-over-par 73 that left him at 11 under on the week at the Masters - the year's first major on Sunday.
The 29-year-old Japanese was seemingly in control until a bogey at the par-five 15th, where his approach shot went in the water behind the green, compounded with a birdie from Schauffele turned his four-stroke cushion into a two-shot lead.
But world number six Schauffele put his tee shot at the par-three 16th into the water and made triple-bogey to fall out of contention.
He finished three shots back of Matsuyama and in a share of third with former champion Jordan Spieth (70).
Matsuyama bogeyed the 16th which left him with a two-shot lead over Zalatoris (70), who was already in the clubhouse at nine under on the week, and went on to close the deal with a par-bogey finish.
The victory by Matsuyama came in his 33rd major championship appearance and ended Zalatoris's impressive bid to become the first Masters debutant to win a Green Jacket since Fuzzy Zoeller accomplished the feat in 1979.
